GSR: Editing - bmsim Simulator

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Long Description (required)

BioNano Molecule SIMulator (BMSIM) explicitly incorporated BioNano data models (BioNano molecule length distribution, FN and FP signals, DNA molecules stretching variations, variation in optical resolution, and fragile sites) and the methods to generate chimeric molecules and assign SNR scores for simulated BioNano molecules. We simulated noisy maps from ‘perturbed’ versions of the reference map. Using genomic sequences (.fasta file) as input, BMSIM simulated noisy maps with five main steps: I) generate BioNano molecules with random fragmentation and fragile site bias model; II) abel nicking sites for BioNano molecules by in silico restriction digestion.Our program supported all available nicking enzymes currently used in BioNano systerm (i.e., Nt.BspQI, Nb.BbvCI, Nb.Bsml and Nb.BsrDI), as well as any artificial nicking sequences that users chose to define; III) incorporate data models for FN sites, FP sites, stretching variations, optical resolution, and chimerism for BioNano molecules; IV) assign SNR and intensity scores for labelling sites; V) iterate for targeted coverage depth. The output of BMSIM is a BNX format text file (.BNX, see example BNX file) which contains molecule map length, label positions, and label signal score, ect.

Attribute Tree Control

Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.

Every sub-attribute is selected
Not all sub-attributes are selected

Attributes

Target
- Type of Simulated Data
  - Genotype at Genetic Markers
  - Diploid DNA Sequence
  - Haploid DNA Sequence
  - RNA
  - Gene Expression
  - Sex Chromosomes
  - Mitochondrial DNA
  - Protein Sequence
  - Sequencing Reads
  - Phenotype
  - Single-Cell Sequencing
  - Bulk Sequencing
  - Proteomics
  - Chromatin Conformation
- Variations
  - Biallelic Marker
  - Multiallelic Marker
  - Single Nucleotide Variation
  - Amino acid variation
  - Microsatellite
  - Insertion and Deletion
  - CNV
  - Inversion and Rearrangement
  - Alternative Splicing
  - Missing Genotypes
  - Genotype or Sequencing Error
  - Ionization
  - Other
Simulation Method
- Standard Coalescent
- Exact Coalescent
- Machine Learning
- Forward-time
- Resample Existing Data
- Phylogenetic
- Gene dropping
- Neural network
- Other
Input
- Data Type
  - Allele Frequencies
  - Empirical
  - Ancestral Sequence
  - Saved simulation
  - Reference genome
  - Other
- File format
  - Arlequin
  - CREATE
  - Fstat
  - GDA
  - Genepop
  - MIGRATE
  - MS
  - SAM or BAM
  - NEXUS
  - Phylip
  - STRUCTURE
  - XML
  - Tree Sequence
  - Program Specific
  - Other
Output
- Data Type
  - Genotype or Sequence
  - Phenotypic Trait
  - Individual Relationship
  - Phylogenetic Tree
  - Demographic
  - Mutation
  - Methylation
  - Gene Expression
  - Protein Expression
  - Linkage Disequilibrium
  - Diversity Measures
  - Fitness
  - Sequencing Reads
    - Illumina
    - Roche 454
    - SOLiD
    - IonTorrent
    - PacBio
    - Nanopore
    - Other
  - Other
- File Format
  - Arlequin
  - Fasta or Fastq
  - Fstat
  - Genepop
  - Linkage
  - MIGRATE
  - MS
  - PED
  - Phylip
  - NEXUS
  - STRUCTURE
  - VCF
  - SAM or BAM
  - Tree Sequence
  - Program Specific
  - Other
- Sample Type
  - Random or Independent
  - Sibpairs, Trios and Nuclear Families
  - Extended or Complete Pedigrees
  - Case-control
  - Longitudinal
  - Other
Phenotype
- Trait Type
  - Binary or Qualitative
  - Quantitative
  - Multiple
- Determinants
  - Single Genetic Marker
  - Multiple Genetic Markers
  - Sex-linked
  - Gene-Gene Interaction
  - Environmental Factors
  - Gene-Environment Interaction
Evolutionary Features
- Demographic
  - Population Size Changes
    - Constant Size
    - Exponential Growth or Decline
    - Logistic Growth
    - Bottleneck
    - Carrying Capacity
    - User Defined
  - Gene Flow
    - Stepping Stone Models
    - Island Models
    - Continent-Island Models
    - Sex or Age-Specific Migration Rates
    - Influenced by Environmental Factors
    - Admixed Population
    - User-defined Matrix
    - Other
  - Spatiality
    - Discrete Models
    - Continuous Models
    - Landscape Factors
- Life Cycle
  - Discrete Generation Model
  - Age structured
  - Overlapping Generation
  - User-Defined transition matrices
- Mating System
  - Random Mating
  - Monogamous
  - Polygamous
  - Haplodiploid
  - Selfing
  - Age- or Stage-Specific
  - Assortative or Disassortative
  - Other
- Fecundity
  - Constant Number
  - Randomly Distributed
  - Individually Determined
  - Influenced by Environment
  - Other
- Natural Selection
  - Determinant
    - Single-locus
    - Multi-locus
    - Codon-based
    - Fitness of Offspring
    - Phenotypic Trait
    - Environmental Factors
  - Models
    - Directional Selection
    - Balancing Selection
    - Multi-locus models
    - Epistasis
    - Random Fitness Effects
    - Disruptive
    - Phenotype Threshold
    - Frequency-Dependent
    - Other
- Recombination
  - Uniform
  - Varying Recombination Rates
  - Gene Conversion Allowed
- Mutation Models
  - Two-allele Mutation Model
  - Markov DNA Evolution Models
  - k-Allele Model
  - Infinite-allele Model
  - Infinite-sites Model
  - Stepwise Mutation Model
  - Codon and Amino Acid Models
  - Indels and Others
  - Heterogeneity among Sites
  - Others
- Events Allowed
  - Population Merge and Split
  - Varying Demographic Features
  - Population Events
  - Varying Genetic Features
  - Change of Mating Systems
  - Other
- Other
  - Phenogenetic
  - Polygenic background
Interface
- Command-line
- Graphical User Interface
- Integrated Development Environment
- Script-based
- Web-based
Development
- Tested Platforms
  - Windows
  - Mac OS X
  - Linux and Unix
  - Solaris
  - Others
- Language
  - C or C++
  - Java
  - R
  - Python
  - Perl
  - Visual Basic
  - Other
- License
  - GNU Public License
  - BSD
  - Creative Commons
  - MIT
  - Other
GSR Certification
- Accessibility
- Documentation
- Application
- Support

Summary of Proposed Changes

Step 2: Review list of proposed attribute addition(s) and subtraction(s).

To Add

To Remove

Can't Find the Attribute You Are Looking For?

If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab.

You may add citations by pmid, add citations by direct entry, remove citations (using the recycling bin icon), and edit citations (using the rarely seen edit icon) that were originally entered by direct entry.

Source From PMID

Summary of Proposed Changes

To Add

To Remove

Current Citations/Applications

[Pubmed ID: 29893801], Chen P, Jing X, Ren J, Cao H, Hao P, Li X, Modelling BioNano optical data and simulation study of genome map assembly., Bioinformatics, 12-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29893801,Primary Citation